Examples with Parameter dr.inference.model.Parameter used on opensource projects

Example 81 with Parameter

use of dr.inference.model.Parameter in project beast-mcmc by beast-dev.

the class ScaledPiecewiseModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
    XMLObject cxo = xo.getChild(EPOCH_SIZES);
    Parameter epochSizes = (Parameter) cxo.getChild(Parameter.class);
    cxo = xo.getChild(TREE_MODEL);
    TreeModel treeModel = (TreeModel) cxo.getChild(TreeModel.class);
    boolean isLinear = xo.getBooleanAttribute("linear");
    return new ScaledPiecewiseModel(epochSizes, treeModel, isLinear, units);
}

Example 82 with Parameter

use of dr.inference.model.Parameter in project beast-mcmc by beast-dev.

the class TwoEpochDemographicModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
    XMLObject cxo = xo.getChild(EPOCH_1);
    DemographicModel demo1 = (DemographicModel) cxo.getChild(DemographicModel.class);
    cxo = xo.getChild(EPOCH_2);
    DemographicModel demo2 = (DemographicModel) cxo.getChild(DemographicModel.class);
    cxo = xo.getChild(TRANSITION_TIME);
    Parameter timeParameter = (Parameter) cxo.getChild(Parameter.class);
    return new TwoEpochDemographicModel(demo1, demo2, timeParameter, units);
}

Example 83 with Parameter

use of dr.inference.model.Parameter in project beast-mcmc by beast-dev.

the class VariableSkylineLikelihoodParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    XMLObject cxo = xo.getChild(POPULATION_SIZES);
    Parameter param = (Parameter) cxo.getChild(Parameter.class);
    cxo = xo.getChild(INDICATOR_PARAMETER);
    Parameter param2 = (Parameter) cxo.getChild(Parameter.class);
    cxo = xo.getChild(CoalescentLikelihoodParser.POPULATION_TREE);
    TreeModel treeModel = (TreeModel) cxo.getChild(TreeModel.class);
    VariableSkylineLikelihood.Type type = VariableSkylineLikelihood.Type.STEPWISE;
    if (xo.hasAttribute(TYPE)) {
        final String s = xo.getStringAttribute(TYPE);
        if (s.equalsIgnoreCase(STEPWISE)) {
            type = VariableSkylineLikelihood.Type.STEPWISE;
        } else if (s.equalsIgnoreCase(LINEAR)) {
            type = VariableSkylineLikelihood.Type.LINEAR;
        } else if (s.equalsIgnoreCase(EXPONENTIAL)) {
            type = VariableSkylineLikelihood.Type.EXPONENTIAL;
        } else {
            throw new XMLParseException("Unknown Bayesian Skyline type: " + s);
        }
    }
    boolean logSpace = xo.getBooleanAttribute(LOG_SPACE);
    Logger.getLogger("dr.evomodel").info("Variable skyline plot: " + type.toString() + " control points");
    return new VariableSkylineLikelihood(treeModel, param, param2, type, logSpace);
}

Example 84 with Parameter

use of dr.inference.model.Parameter in project beast-mcmc by beast-dev.

the class BayesianSkylineGibbsOperatorParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
    final double lowerBound = xo.getAttribute(LOWER, 0.0);
    final double upperBound = xo.getAttribute(UPPER, Double.MAX_VALUE);
    final boolean jeffreysPrior = xo.getAttribute(JEFFREYS, true);
    boolean exponentialMarkovPrior = xo.getAttribute(EXPONENTIALMARKOV, false);
    double shape = xo.getAttribute(SHAPE, 1.0);
    boolean reverse = xo.getAttribute(REVERSE, false);
    int iterations = xo.getAttribute(ITERATIONS, 1);
    BayesianSkylineLikelihood bayesianSkylineLikelihood = (BayesianSkylineLikelihood) xo.getChild(BayesianSkylineLikelihood.class);
    // This is the parameter on which this operator acts
    Parameter paramPops = (Parameter) xo.getChild(Parameter.class);
    Parameter paramGroups = bayesianSkylineLikelihood.getGroupSizeParameter();
    final int type = bayesianSkylineLikelihood.getType();
    if (type != BayesianSkylineLikelihood.STEPWISE_TYPE) {
        throw new XMLParseException("Need stepwise control points (set 'linear=\"false\"' in skyline Gibbs operator)");
    }
    return new BayesianSkylineGibbsOperator(bayesianSkylineLikelihood, paramPops, paramGroups, type, weight, lowerBound, upperBound, jeffreysPrior, exponentialMarkovPrior, shape, reverse, iterations);
}

Example 85 with Parameter

use of dr.inference.model.Parameter in project beast-mcmc by beast-dev.

the class RandomWalkIntegerNodeHeightWeightedOperatorParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
    double d = xo.getDoubleAttribute(WINDOW_SIZE);
    if (d != Math.floor(d)) {
        throw new XMLParseException("The window size of a " + RANDOM_WALK_INT_NODE_HEIGHT_WGT_OP + " should be an integer");
    }
    int windowSize = (int) d;
    Parameter parameter = (Parameter) xo.getChild(Parameter.class);
    Parameter internalNodeHeights = (Parameter) xo.getElementFirstChild(INTERNAL_NODE_HEIGHTS);
    return new RandomWalkIntegerNodeHeightWeightedOperator(parameter, windowSize, weight, internalNodeHeights);
}